ArticleAlgorithms for molecular biology : AMB2010
An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.
Article in Algorithms for molecular biology : AMB, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 58 citations in OpenAlex.
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- A conserved hymenopteran-specific family of cytochrome P450s protects bee pollinators from toxic nectar alkaloids.Science advances · 2023Article
- Functional Classification and Characterization of the Fungal Glycoside Hydrolase 28 Protein Family.Journal of fungi (Basel, Switzerland) · 2022Article
- Structure-function analysis of Sedolisins: evolution of tripeptidyl peptidase and endopeptidase subfamilies in fungi.BMC bioinformatics · 2018Article
- Molecular dynamics and structure function analysis show that substrate binding and specificity are major forces in the functional diversification of Eqolisins.BMC bioinformatics · 2018Article
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- An evolutionary roadmap to the microtubule-associated protein MAP Tau.BMC genomics · 2016Article
- AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators.Journal of molecular biology · 2016Article
- Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis.Frontiers in microbiology · 2016Article
- Evolutionary and Functional Relationships in the Truncated Hemoglobin Family.PLoS computational biology · 2016Article
- Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.Bioinformatics (Oxford, England) · 2015Article
- Basis for substrate recognition and distinction by matrix metalloproteinases.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Molecular evolution of the enzymes involved in the sphingolipid metabolism of Leishmania: selection pressure in relation to functional divergence and conservation.BMC evolutionary biology · 2014Article
- Extensive expansion of A1 family aspartic proteinases in fungi revealed by evolutionary analyses of 107 complete eukaryotic proteomes.Genome biology and evolution · 2014Article
- Evolutionary and structural analyses of mammalian haloacid dehalogenase-type phosphatases AUM and chronophin provide insight into the basis of their different substrate specificities.The Journal of biological chemistry · 2014Article
- Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota.Frontiers in microbiology · 2014Article
- Formin' cellular structures: Physiological roles of Diaphanous (Dia) in actin dynamics.Communicative & integrative biology · 2013Review
- Engineering the acyltransferase substrate specificity of assembly line polyketide synthases.Journal of the Royal Society, Interface · 2013Review
- PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity.BMC bioinformatics · 2013Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins, that is, prediction of exact specificity to a ligand or, more broadly, to a binding partner of any kind.
resultsWe present a method, SDPclust, for identification of protein functional subfamilies coupled with prediction of specificity-determining positions (SDPs). SDPclust predicts specificity in a phylogeny-independent stochastic manner, which allows for the correct identification of the specificity for proteins that are separated on a phylogenetic tree, but still bind the same ligand. SDPclust is implemented as a Web-server http://bioinf.fbb.msu.ru/SDPfoxWeb/ and a stand-alone Java application available from the website.
conclusionsSDPclust performs a simultaneous identification of specificity determinants and specificity groups in a statistically robust and phylogeny-independent manner.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.